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This paper presents a detailed study of a water adlayer adsorbed on Pt(111) and Rh(111) surfaces using periodic density functional theory methods. The interaction between the metal surface and the water molecules is assessed from molecular dynamics simulation data and single point electronic structure calculations of selected configurations. It is argued that the electron bands around the Fermi level of the metal substrate extend over the water adlayer. As a consequence in the presence of the water layer the surface as a whole still maintains its metallic conductivity-a result of a crucial importance for understanding the process of electron transfer through the water/metal interface and electrochemical reactions in particular. Our results also indicate that there exists a weak bond between the hydrogen of the water and the Rh metal atoms as opposed to the widespread (classical) models based on purely repulsive interaction. This suggests that the commonly used classical interactions potentials adopted for large scale molecular dynamics simulations of water/metal interfaces may need revision. Two adsorption models of water on transition metals with the OH bonds pointing towards or away of the surface are also examined. It is shown that due to the very close values of their adsorption energies one should consider the real structure of water on the surface as a mixture of these simple "up" and "down" models. A model for the structure of the adsorbed water layer on Rh(111) is proposed in terms of statistical averages from molecular dynamics simulations.

In this paper we present the implementation of the two-component scaled zeroth-order regular approximation (ZORA) method in the molecular electronic structure package GAMESS-UK. It is the first application of this method, which was earlier investigated in the context of density functional theory, in molecular ab initio basis set calculations. The performance of the method is tested in atomic calculations, which we can compare with numerical results, on xenon and radon and in molecular calculations on the molecules AgH, HI, I2, AuH, TlH, and Bi2. In calculations on the I2 molecule we investigated the effect of the different approaches regarding the internal Coulomb matrix used in the ZORA method. For the remaining molecules we computed harmonic frequencies and bond lengths. It is shown that the scaled ZORA approach is a cost-effective alternative to the Dirac–Fock method.

Three high-level correlated ab initio studies have recently been performed on the electronic absorption spectrum of free base porphin (FBP), but significant differences between the various assignments of the low-lying bands remain. In view of the importance of FBP as the basic building block of the porphyrins, further reliable results are evidently required and are provided here, using time-dependent density functional theory (TDDFT). Our results strongly support the recent CASPT2 interpretation which is consistent with the traditional interpretation, stating that the intense B band (or Soret band) is due to the two close-lying excitations 2 1B2u and 2 1B3u. As in the CASPT2 paper, we attribute all low-lying bands to pairs of 1B2u–1B3u excitations. The interpretation of the combined B–N band system is discussed in some detail. The effects of basis set, geometry, and choice of exchange-correlation potential are considered as well.

In quantum-mechanical/molecular-mechanical (QM/MM) treatment of chemical reactions in condensed phases, one solves the electronic Schrodinger equation for the solute (or an active site) under the electrostatic field from the environment. This Schrodinger equation depends parametrically on the solute nuclear coordinates R and the external electrostatic potential V. This fact suggests that one may use R and V as natural collective coordinates for describing the entire system, where V plays the role of collective solvent variables. In this paper such an (R,V) representation of the QM/MM canonical ensemble is described, with particular focus on how to treat charge transfer processes in this representation. As an example, the above method is applied to the proton-coupled electron transfer of a ubiquinol analog with phenoxyl radical in acetonitrile solvent. Ab initio free-energy surfaces are calculated as functions of R and V using the reference interaction site model self-consistent field method, the equilibrium points and the minimum free-energy crossing point are located in the (R,V) space, and then the kinetic isotope effects (KIEs) are evaluated approximately. The results suggest that a stiffer proton potential at the transition state may be responsible for unusual KIEs observed experimentally for related systems.

Item does not contain fulltext Transport properties of molecular junctions are notoriously expensive to calculate with ab initio methods, primarily due to the semi-infinite electrodes. This has led to the introduction of different approximation schemes for the electrodes. For the most popular metals used in experiments, such as gold, the wide-band limit (WBL) is a particularly efficient choice. In this paper, we investigate the performance of different WBL schemes relative to more sophisticated approaches including the fully self-consistent non-equilibrium Green's function method. We find reasonably good agreement between all schemes for systems in which the molecule (and not the metal-molecule interface) dominates the transport properties. Moreover, our implementation of the WBL requires negligible computational effort compared to the ground-state density-functional theory calculation of a molecular junction. We also present a new approximate but efficient scheme for calculating transport with a finite bias. Provided the voltage drop occurs primarily inside the molecule, this method provides results in reasonable agreement with fully self-consistent calculations.

The hydrogen storage system LiH + NH(3) ↔ LiNH(2) + H(2) is one of the most promising hydrogen storage systems, where the reaction yield can be increased by replacing Li in LiH with other alkali metals (Na or K) in order of LiNaK. In this paper, we have studied the alkali metal M (M = Li, Na, K) dependence of the reactivity of MH with NH(3) by calculating the potential barrier of the H(2) desorption process from the reaction of an M(2)H(2) cluster with an NH(3) molecule based on the ab initio structure optimization method. We have shown that the height of the potential barrier becomes lower in order of Li, Na, and K, where the difference of the potential barrier in Li and Na is relatively smaller than that in Na and K, and this tendency is consistent with the recent experimental results. We have also shown that the H-H distance of the H(2) dimer at the transition state takes larger distance and the change of the potential energy around the transition state becomes softer in order of Li, Na, and K. There are almost no M dependence in the charge of the H atom in NH(3) before the reaction, while that of the H atom in M(2)H(2) takes larger negative value in order of Li, Na, and K. We have also performed molecular dynamics simulations on the M(2)H(2)-NH(3) system and succeeded to reproduce the H(2) desorption from the reaction of Na(2)H(2) with NH(3).

The reactivity and spectra of formaldehyde isomers and dimeric complexes between them are studied with ab initio methods. A large number of complexes between H2CO, trans-HCOH, cis-HCOH is calculated. Infrared and Raman spectra of (H2CO)2 are calculated with relatively simple methods using spectroscopic masses and scaled force constants. In this way, the structure of dimers in matrices can be deduced. Hydroxycarbene (HCOH) plays a key role in a model that explains a large number of experimental facts of the nonzero pressure photochemistry. Hydroxycarbene forms complexes with H2CO; the stabilization is due to classical hydrogen bonds. HCOH is a new example of an ambiphilic carbene. Addition products are formed from HCOH···H2CO complexes. The calculations show that, in agreement with matrix experiments, glycoaldehyde and methanol are easily formed. The formation of trans-HCOH occurs through a dimeric interaction with the shifting hydrogen. This bimolecular process is 9.6 kcal/mol (6–31G*) in favor of the unimolecular conversion. cis-HCOH might be formed via a nonplanar transition state, where also stabilization at the carbenic center is possible. When higher concentrations of HCOH are available, a hydrogen exchange mechanism easily transfers hydroxycarbene back to H2CO. Several experiments are suggested in this paper; notably, molecular beam and isotopic-mixture experiments will give useful information. The involvement of HCOH in the light-induced formose reaction is suggested.

This paper reports an ab initio CI calculation of the radiationless decay of the formaldehyde 1A2 state. First we derive quantitative conditions, which a basis set must satisfy if it is to be used for describing radiationless decay. We checked these conditions for the formaldehyde molecule and found them to be satisfied for the adiabatic Born–Oppenheimer set used in the calculation. We then derive a general equation for the coupling elements resulting from this basis set. With the method used, rotational coupling could be treated completely equivalent with vibrational coupling; this rotational coupling turned out to be not important in formaldehyde however. The coupling elements for D2CO are a factor 10 smaller than the corresponding ones in H2CO. The results of the calculation show, that the internal conversion in formaldehyde is an example of the so-called resonance case. Therefore the decay cannot be described by the model proposed by Yeung and Moore, where S1¿S0 internal conversion is the rate determining step in the photodissociation. Finally, we discuss the applicability of the ’’golden rule’’ in describing radiationless decay.

This paper reports an ab initio CI calculation of the radiative 1A1¿1A2 transition of H2CO and D2CO. Throughout the calculation the electronic wavefunctions and transition moments are explicitly calculated as functions of the nuclear geometry, contrary to the conventional Herzberg–Teller approach. The evaluation of the vibrational wavefunctions and integrals was made numerically. The results show that the excited state frequency for mode 3 has to be reassigned and that the calculated vibrational structure agrees well with the experimental intensities.